Thesis (Ph. D.)--Rhodes University, 2004. / Title from PDF t.p. (viewed on May 2, 2006). Includes bibliographical references (p. 159-206).

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Typescript. Includes vita and abstract. Bibliography: Includes bibliographical references (leaves 53-56).

Manipulation or control of the microbiological aquaculture environment has been identified as an important focus area for future hatchery development. Subsequently, alternatives to obtain control of the microbiological environment are being sought of which the field of probiotics appears highly promising. Probiotics are usually selected based on various in vitro characteristics, however, the methods used differ and are sometimes unsuccessful due to poor experimentation. The aim of this work is to contribute towards the development of a protocol for the in vitro screening of bacterial candidate probiotics for marine fish larviculture. To reduce the number of candidate probiotics to be tested in vivo, various in vitro experiments need to be conducted, each screening for a particular mode of action – antagonism towards pathogen through production of antimicrobial compounds, growth and attachment to fish intestinal mucus, and the production of other beneficial compounds such as vitamins, fatty-acids and digestive enzymes. A total of 108 bacteria species were isolated from the digestive tract of the adult common clownfish, Amphiprion percula to screen for potential probiotics to be used in clownfish larval rearing. The antagonistic compounds assay identified twelve isolates which showed antagonism towards two or more aquatic pathogens. This was followed by an in vitro test that involved growing the organisms in fish intestinal mucus and modeling their growth parameters. A ranking index (RI) was developed using the lag period (λ) and doubling time (td) of the organism, where (1over λ x td) x 100. Five candidate probionts (AP1-AP5) with varied growth parameters were used for further in vitro experiments. The attachment to mucus assay introduced a novel tool for quantifying competition for attachment sites between candidate probionts and pathogens on mucus. Candidate probiont Pseudoalteromonas AP5 reduced the attachment ability of Vibrio alginolyticus when added before the pathogen and partially out-competed the pathogen for attachment sites when added second. In vitro screening for the production of beneficial compounds tested the candidate probiotics’ ability to produce digestive enzymes - trypsin, lipase and alkaline phosphatase as well as carotenoids and vitamin C. Candidate probiont Pseudoalteromonas AP5 produced high levels of the enzymes (98.2, 34.1 and 91.3 mU product liberated.ml⁻¹, respectively) and contained carotenoids while Kocuria AP4 contained carotenoids but produced low quantities of enzymes (7.8, 0 and 59 mU product liberated.ml⁻¹, respectively). None of the candidate probiotics produced vitamin C. To eliminate potential pathogenic or toxic candidate probionts, Artemia nauplii were exposed to each candidate probiont and the percentage Artemia mortality after 24-hours was determined. Candidate probiont AP2 caused high mortality of Artemia nauplii (98.4%) and was excluded from further studies. Identification of candidate probionts AP3-AP5 was performed using 16S-rDNA molecular techniques and the bacteria were assigned the names Bacillus AP3, Kocuria AP4 and Pseudoalteromonas AP5, respectively. Two methods of larval probiont delivery were tested – attachment to Artemia, and in-water delivery. Attachment to Artemia was high for both Kocuria AP4 and Pseudoalteromonas AP5 (7.2 x10³ and 2.7x10⁴ bacteria.nauplius⁻¹, respectively) while the in-water viability experiment showed that Kocuria AP4 comprised 23.9% of the total culturable water microflora after 24 hours while Pseudoalteromonas AP5 contributed 100%. To validate the findings from the in vitro experiments, in vivo trials using clownfish larvae were performed. Of the four candidate probiotics tested, only Kocuria AP4 showed potential to increase larval survival. In vitro tests produced a better understanding of the possible mode of action and strategies of competition between bacteria, however, the number of criteria in which a candidate probiont is successful in vitro may not be the best predictor for its effectiveness in vivo. Commercial studies that reduce between-treatment variation are required to test predictions about the most suitable probiont or combinations thereof.

Heritabilties and genetic correlations using Individual Animal Model, (IAM), analysis for weight, length and survivability were determined in both freshwater and saltwater rearing of s0 and si1 coho, (Oncorhynchus kisutch). The most important trait to salmon farmers is the saltwater market weight which was found to have heritability estimates of 0.21 and 0.45 for the s1 and s0 smolts. Estimates of heritability for survival were high, (0.29 and 0.21) for both s0 and s1 rearing strategies. Genetic correlations between freshwater and saltwater size were small, (0.33 to 0.59) indicating selection for market weight should be done during the saltwater market weight window. Significant differences were found for weight and length between strains during freshwater and saltwater rearing for both s0 and si1 coho. The northern strains, (Kitimat, Bella Coola and Pallant Creek) were significantly larger in weight and length thanthe southern strains, (Big Qualicum and Robertson Creek). The Kitimat strain was larger in weight and length than the Bella Coola and Pallant Creek strains but lower than these two strains for percent survivability. When comparing fish from the Kitimat strain reared on both a s0 and s1 rearing strategy, it was found that the s1 fish were significantly larger than the s0 fish at the market weight window. / Land and Food Systems, Faculty of / Graduate

Feed accounts for 40% to 60% of the operating costs of Pacific salmon farms. Presently, commercial diets for Pacific salmon in seawater are formulated according to the nutrient requirements of juvenile chinook salmon and digestibility information derived from studies on rainbow trout in fresh water. Information on feedstuff digestibility by Pacific salmon is completely lacking, regardless of life history stage. Hence, this thesis was undertaken to determine the apparent digestibility of organic matter, crude protein and energy in conventional and novel feedstuffs using post-juvenile chinook salmon (Oncorhynchus tshawytscha) in seawater. The validity of determining apparent nutrient digestibility using the "Guelph system" of fecal collection and chromic oxide (Cr₂O₃) as the indigestible indicator in the diet was assessed in experiment I. In this regard, fecal samples were collected either from a settling column affixed to each novelly designed digestibility tank at 6 and 18 hour intervals or directly from the terminal section of the intestinal tract by stripping or intestinal dissection. Digestibility coefficients were noted to be significantly increased (P<0.001) when the feces remained in the water for 18 hours instead of 6 hours, owing to nutrient leaching. The collection of feces directly from the fish resulted in lower digestibility coefficients than those found when feces were obtained from the "Guelph system". This was attributed to a flaw in the design of the digestibility tank drain system, whereby the feces did not settle quickly into the collection column. The problem was rectified before conducting the subsequent experiments described below. In three additional experiments on chinook salmon in seawater, the overall goal was to ascertain the organic matter, crude protein and energy digestibility coefficients and the digestible energy values for commercial sources of fish meal (herring meal, anchovy meal, menhaden meal, Norwegian low temperature fish meal), poultry by-product meal (two suppliers), feather meal, blood meal, dried whey, canola meal, soybean meal, soybean protein isolate, extruded wheat and wheat middlings. Also, three novel sources of rapeseed protein products (two types of glucosinolate-free canola meal and rapeseed protein concentrate) were evaluated in this regard. The initial minimum size of the chinook in these studies varied between 10.3 g and 40.5 g. The digestibility tank complex consisted of 27 open-circuit 150 L fiberglass digestibility tanks, each supplied with aerated, 8.0°C to 12.5°C filtered seawater at a rate of 6 L/min. The fish were fed by hand twice daily to satiation either a reference diet or a test diet (70% reference : 30% test ingredient). In some instances involving plant protein products, the test ingredient was included at two dietary levels (15% and 30%). Within each test, each diet treatment was assigned to three groups of fish using a completely random or randomized complete block design. Chromic oxide (0.5%) was included in all diets as the indigestible marker. At the end of each experiment, fish were sacrificed and their feces were removed either by stripping or intestinal dissection for comparisons of methodology. In general, the fish meals had higher available energy content for chinook salmon than the other animal and plant protein sources assessed. The importance of screening feedstuffs for potential nutritive value by digestibility measurements was particularly evident from an examination of the digestibility coefficients obtained for menhaden meal versus the other fish meal sources, the two sources of poultry by-product meal, wheat products, canola products and blood meal in this study. The assessment of soybean products, regardless of dietary inclusion level (15% or 30%), could not be ascertained in chinook salmon because of poor diet acceptance. Canola protein sources appear highly promising as partial or complete (in the case of rapeseed protein concentrate) replacements of fish meal, based on digestibility assessment. The use of the "Guelph system" for fecal collection resulted in organic matter digestibility coefficients similar to those obtained by intestinal dissection. Thus, nutrient leaching must have been minimal with the "Guelph system" and it is concluded that this is a satisfactory procedure for digestibility assessment using chinook salmon in seawater. / Land and Food Systems, Faculty of / Graduate

Data were collected from participating grow-out salmon farmers, processors, and the B.C. Salmon Farmers' Association, through interviews, and utilized to define a base farm. A microcomputer based spreadsheet model was constructed to capture the important biological and economic variables. The model details the operating costs and returns of a farm for five years, and assumes operating costs are consistent with the fifth year to provide cash flows for a total of 20 years. The financial analysis includes an examination of the net present values, the net farm income, and the internal rate of return. Results indicate that the base farm is a viable investment at a 6.9% discount rate. A sensitivity analysis is utilized to determine the critical variables in the operation of a grow-out salmon farm. The most sensitive variable turned out to be the growth rate of salmon. The base farm was found to be vulnerable to economic variables such as the product price, and the feed price. Other important biological variables are the feed conversion ratio and the mortality rate, both of which have a significant effect on the viability of the base farm. / Land and Food Systems, Faculty of / Graduate

Salmon aquaculture is the rearing of salmonids for commercial purposes. These practices are typically carried out in saltwater farms located in coastal waters. The process of siting these facilities requires identifying and selecting areas that are economically, socially and environmentally suitable to locate them. Siting salmon aquaculture facilities has become a controversial resource management issue in British Columbia (B.C.), where distance-based criteria ultimately determine the location of these facilities. This thesis focuses on providing insights and concepts to inform and examine the salmon aquaculture facility siting process in B.C. It is argued that regulatory processes and outcomes in the context of a new industry could respond to mechanisms and factors that shape governmental agendas, illustrating how policy can behave reactively rather than in a precautionary manner. In this case, the outcomes of such reactive policies are reflected in siting criteria that yield implicit environmental and socio-economic disadvantages and tradeoffs. This way, siting criteria derive from expert judgements based on best available information while their associated uncertainties may lead to consider less-desirable sites while underestimating or overestimating risks, and overlooking important regional objectives, cumulative impacts and stakeholder values. The thesis further suggests that the future evolution of the salmon aquaculture facility siting process in B.C. could benefit from siting processes that have already been developed and implemented by other sectors. Different lines of reasoning that deal with processes of public negotiation, analytical decision-making and a systems' approach are explored as ways by which the salmon aquaculture facility siting process could evolve in the future toward creating more comprehensive policy. / Science, Faculty of / Resources, Environment and Sustainability (IRES), Institute for / Graduate

Between 1985 and 1995, government agencies and interest groups interacted in a recurring cycle of moratoria and reviews in attempts to resolve a wide variety of environmental, economic and social concerns about salmon farming while making policies to manage the development of the new industry in British Columbia. Using policy community theory, this thesis analyzes how the community members developed the salmon farming policy framework. Then, drawing on the recommendations that were already advanced by aquaculture planners from the early 1980s, the thesis evaluates the policy framework that exists today. Depending upon their power resources and their position within the policy community, the members of the community used different methods to influence the policy process. The members of the sub-government maintained the status quo by using methods such as restricting the access for interest groups to the policy process and limiting the flow of information to the attentive public. The members of the attentive public increased their power by forming coalitions and putting forward a common policy statement to the public and government. Maintaining the status quo became difficult when the New Democratic Party (NDP) government came to power. In revising provincial environmental policies , the NDP changed the relative influence of the government agencies in the sub government. These changes increased conflict among agencies which the government addressed by undertaking an environmental assessment and a public policy review. The B.C. salmon farming policy community is identified as a pressure pluralist community which emerges when jurisdictional responsibility is fragmented among a number of agencies and no mediating mechanism exists to bring together the members of the community. As a result , the community tends to make short term policy and functions without a long term strategy. The thesis concludes with six recommendations designed to increase the access and input of all those who want to participate in the policy process, to address the diversity of issues raised within the policy community, to insure social accountability when interest groups implement policy , and to fill the gaps in the existing policy framework. / Applied Science, Faculty of / Community and Regional Planning (SCARP), School of / Graduate

M.Sc. / Please refer to full text to view abstract